3CF6

Structure of Epac2 in complex with cyclic-AMP and Rap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B

Rehmann, H.Arias-Palomo, E.Hadders, M.A.Schwede, F.Llorca, O.Bos, J.L.

(2008) Nature 455: 124-127

  • DOI: 10.1038/nature07187
  • Also Cited By: 1C1Y

  • PubMed Abstract: 
  • Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined ...

    Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.


    Related Citations: 
    • Structure and regulation of the cAMP-binding domains of Epac2
      Rehmann, H.,Prakash, B.,Wolf, E.,Rueppel, A.,de Rooij, J.,Bos, J.L.,Wittinghofer, A.
      (2003) Nat.Struct.Mol.Biol. 10: 26
    • Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state
      Rehmann, H.,Das, J.,Knipscheer, P.,Wittinghofer, A.,Bos, J.L.
      (2006) Nature 439: 625


    Organizational Affiliation

    Department of Physiological Chemistry, Centre for Biomedical Genetics and Cancer Genomics Centre, University Medical Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands. h.rehmann@UMCutrecht.nl




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rap guanine nucleotide exchange factor (GEF) 4
E
694N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rap-1b
R
167Homo sapiensMutation(s): 0 
Gene Names: RAP1B
Find proteins for P61224 (Homo sapiens)
Go to Gene View: RAP1B
Go to UniProtKB:  P61224
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SP1
Query on SP1

Download SDF File 
Download CCD File 
E
6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL
SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE
C10 H12 N5 O5 P S
SMPNJFHAPJOHPP-LHKKBNDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 125.367α = 90.00
b = 149.025β = 90.00
c = 225.291γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-05
    Type: Derived calculations